Can you give me a piece of advise of the network sructure that would be suitable for my task?
Instead of NNs, you can use RANSAC algorithm to calculate homography matrix, but first you need to find feature points. However, if your images are blob-like, you may not get such a successful results. Here some presentations for better understanding: cs.umd notes and csail.mit notes
(Also, there might be better image processing tools.)